The Russian diplomat who was ordered to leave the Baltic state is suspected of "illegal intelligence activities" and of trying to influence Lithuania's position in the ongoing row between Russia and Georgia, BNS said on Sunday, citing unnamed sources in the foreign ministry.
The BNS report also said that Russia was poised to expel a Lithuanian diplomat from Russia in retaliation.
The presidents of Lithuania, Poland and Ukraine expressed concern this week about the increasingly bitter diplomatic spat between Moscow and Tbilisi, which was sparked when Georgia arrested four Russian officers and accused them of spying.
The leaders of the three countries - of which two, Lithuania and Ukraine, are former Soviet republics, like Georgia - also offered to mediate in the conflict.
Petras Vaitiekunas, the Lithuanian foreign minister, refused to comment on the report.
"I can neither confirm nor deny these reports," Vaitiekunas said, adding that there would be no official statement from the foreign ministry on the alleged diplomatic row between Vilnius and Moscow.